For multi-input multi-output (MIMO) plants, the model-based control system has more than one primary target to control in different operating conditions. In general, the multiple inputs are the control handles driven by the actuators. The model-based control system determines the input commands to multiple actuators in a plant in order to control multiple plant outputs to achieve multiple control objectives under different operating conditions. By way of example, a plant may be a jet engine wherein multiple actuators control the processes of the jet engine to produce outputs such as fan speed, pressure ratios, nozzle position or core temperature which correspond to multiple control objectives such as thrust, fan operability and/or core operability, and fuel consumption. Actuators in MIMO control system may be constrained for various reasons resulting in loss of a certain level of control effects or complete control effects on plant outputs. Model-based control performance is dependent on the plant model and if the plant model cannot capture certain plant dynamic changes included in or induced by the constrained actuator(s), then the model-based control resulting from the model may not control the plant with such changes properly or stably.